1. Panorama Public and Panorama AutoQC Tutorial Webinar #11 With Vagisha Sharma (Lead Developer - Panorama) Josh Eckels (Lead Panorama Developer – LabKey)

2. Agenda  Welcome from the Skyline team!  Panorama Public and Panorama AutoQC  Quick intro with Brendan MacLean  Panorama Public with Vagisha Sharma  Introducing Panorama, PanoramaWeb and Panorama Public  Tutorial  Panorama QC with Josh Eckels  Introducing Panorama as a QC data store  Tutorial  AutoQC automated pipeline with Vagisha Sharma  Audience Q&A – submit questions to Google Form: https://skyline.gs.washington.edu/labkey/qa4skyline.url

3. Vagisha Sharma MacCoss Lab Targeted Proteomics Knowledge Base Skyline Webinar # 11

4. …in a nutshell Panorama is a web application for storing, sharing, analyzing and reusing targeted methods created and refined with Skyline.

5. Motivation for Panorama Skyline enabled rapid generation of targeted methods Wide adoption of Skyline led to a need to organize and manage Skyline documents o Facilitate data sharing o Search across experiments o Reuse information from prior experiments

6. Panorama Data management system for Skyline documents o Search and review a large body of data Integration with Skyline o Store the complete Skyline document data model o Direct export from Skyline to Panorama Share data with collaborators o Users can set permissions on the data o Private, public or access to selected collaborators Web browser interface for viewing, searching and analyzing results o Share data with collaborators not using Skyline o Get a quick overview of results Build chromatogram libraries o Curated assays to inform future experiments QC folders o Track instrument performance over time and identify problems

7. Skyline/Panorama Workflow

8. PanoramaWeb Panorama is locally installable o Part of LabKey Server – an open source biomedical data management platform o Free and open source (Apache 2.0) PanoramaWeb : Panorama server hosted by the MacCoss lab at the University of Washington o Free projects for over 100 labs o Project owners have full control over their projects o Organize folders in the project o Set permissions Several projects on PanoramaWeb have supplementary data associated with published manuscripts o Researchers make the data public to fulfill journal submission requirements

9. PanoramaWeb Published data is spread out across researcher projects o No centralized, searchable location of published supplementary data Researchers retain control over data o Data may be deleted or altered post publication

10. Panorama Public Public repository on PanoramaWeb o Managed by PanoramaWeb site administrators Data already in a project on PanoramaWeb can be “published” to Panorama Public Single location that can be searched Data on Panorama Public is read-only to original authors o Available in its original form as it was intended for publication Permanent location of data that can be referenced in publications o Researchers create a permanent link for the data

11. Publication Protocol STEP 1 Upload from Skyline to PanoramaWeb

12. Publication Protocol STEP 2

13. Publication Protocol

14. Folder in researcher’s project on PanoramaWeb Folder on Panorama Public after copy READ ONLY Copy

15. Demo Go to panoramaweb.org

16. Publication Protocol

17. Quality Control Measure QC peptide every few runs to ensure expected chromatography and instrument performance Import QC runs into a Skyline document on the instrument computer o Look at retention time, peak areas in Skyline o Run SProCoP to detect and visualize potential problems o External Skyline tool o Developed by the Bereman lab (NCSU) Need to be at the instrument computer or have access to the Skyline document with QC runs Panorama QC workflow o Automate importing QC runs and uploading to Panorama o Track instrument performance in Panorama QC folders

18. Learn More  Webinar #12: Isotope Labeled Standards in Skyline  Tuesday, December 1 st - Tina Ludwig and Ariel Bensimon  Workshop in Puerto Vallarta, November 8 & 9  Weeklong Course at IIT-Bombay  December 10-14  Weeklong Courses 2016  ETH, Zurich – February 8-12 – Register now!  Buck Institute, San Francisco – March 7-11 – Register soon  Northeastern University, Boston – May 2-6  University of Washington, Seattle – July 18-22

19. Questions?  Ask any questions you have on modifications in Skyline at the following form: http://tinyurl.com/QA4Skyline http://tinyurl.com/QA4Skyline  Take the post-webinar survey: http://tinyurl.com/Survey4Webinar

20. Tutorial Webinar #11 This ends this Skyline Tutorial Webinar. Please give us feedback on the webinar at the following survey: http://tinyurl.com/Survey4Webinar A recording of today’s meeting will be available shortly at the Skyline website. We look forward to seeing you at a future Skyline Tutorial Webinar.